chr14-25277153-C-T

Variant names:

• chr14-25277153-C-T
• rs10498281
• ENST00000837960.1:n.380-1870C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000837960.1(ENSG00000309034):​n.380-1870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,944 control chromosomes in the GnomAD database, including 16,732 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (16732 hom., cov: 32)
• Consequence: ENSG00000309034 ENST00000837960.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 2 publications found

Genes affected

ENSG00000309034 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309034	ENST00000837960.1	n.380-1870C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71191 AN: 151826 Hom.: 16704 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.468

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.469 AC: 71263 AN: 151944 Hom.: 16732 Cov.: 32 AF XY: 0.471 AC XY: 35015 AN XY: 74274

African (AFR) AF: 0.461 AC: 19109 AN: 41450

American (AMR) AF: 0.466 AC: 7113 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1451 AN: 3462

East Asian (EAS) AF: 0.498 AC: 2568 AN: 5160

South Asian (SAS) AF: 0.484 AC: 2336 AN: 4822

European-Finnish (FIN) AF: 0.492 AC: 5179 AN: 10528

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32053 AN: 67936

Other (OTH) AF: 0.472 AC: 996 AN: 2112

Alfa AF: 0.456 Hom.: 1920

Bravo AF: 0.466

Asia WGS AF: 0.497 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.68
PhyloP100		-0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10498281; hg19: chr14-25746359;